Contents

Brain data

Brain data

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI

Code imports

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

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Load data plot it

dataset.load()

dataset.data_type

'brain'

fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'

fig_gm.display('jupyter-book', tissue = 'GM')

White matter qMRI

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'

fig_wm.display('jupyter-book', tissue = 'WM')

Spine

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

dataset.load()
dataset.data['T1w']

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Subject Session Timestamp SCT Version Filename Slice (I->S) VertLevel MEAN(area) STD(area) MEAN(angle_AP) ... STD(diameter_AP) MEAN(diameter_RL) STD(diameter_RL) MEAN(eccentricity) STD(eccentricity) MEAN(orientation) STD(orientation) MEAN(solidity) STD(solidity) SUM(length)
1 1 1 2021-06-09 23:24:10 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 31:75 2:3 67.680431 1.598728 -4.254822 ... 0.225578 10.843164 0.307774 0.680936 0.039585 2.149545 1.734302 0.980308 0.009615 36.167347
6 1 2 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 47:86 2:3 67.511930 1.726861 -6.577358 ... 0.186145 10.874612 0.275935 0.690540 0.031751 2.855729 1.967201 0.977647 0.008612 32.528253
0 1 3 2021-06-09 23:24:08 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:93 2:3 64.109061 3.127582 -4.670983 ... 0.464761 10.640776 0.333651 0.690605 0.054994 3.202127 2.184708 0.976971 0.007494 34.565242
8 2 1 2021-06-09 23:41:15 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 1:38 2:3 66.455289 4.204379 0.095829 ... 0.684070 11.992443 0.585042 0.794791 0.061804 2.234122 1.464966 0.963074 0.016533 31.424022
10 2 2 2021-06-09 23:41:24 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 12:50 2:3 73.688109 2.833139 -0.068322 ... 0.406465 12.065046 0.492764 0.756302 0.053939 2.367144 1.803792 0.966030 0.009791 32.356730
15 2 3 2021-06-09 23:50:43 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 3:39 2:3 73.905494 2.073274 -0.691532 ... 0.368828 12.371408 0.639116 0.780126 0.052688 1.694898 1.187327 0.963111 0.014391 30.534960
12 2 4 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 9:46 2:3 69.405673 4.568637 -0.749008 ... 0.543059 12.227376 0.665839 0.796428 0.053488 2.145301 1.623586 0.958420 0.020529 31.442066
9 3 1 2021-06-09 23:41:20 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 51:85 2:3 59.927681 1.980624 -0.778617 ... 0.334499 10.086060 0.232852 0.658816 0.049798 2.475063 1.644264 0.972640 0.009458 28.297791
13 3 2 2021-06-09 23:41:42 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 33:66 2:3 60.228814 1.776652 -1.464265 ... 0.247391 10.486967 0.214164 0.716856 0.033921 1.850661 1.538691 0.966100 0.007298 27.236579
11 3 3 2021-06-09 23:41:39 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 60.621684 1.733616 -0.009478 ... 0.358365 10.632869 0.308162 0.726909 0.049649 1.681134 1.217510 0.970807 0.010769 28.389363
16 3 4 2021-06-09 23:55:17 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 40:74 2:3 59.915665 2.030933 -2.222570 ... 0.296578 10.445562 0.243935 0.716104 0.038919 2.551453 2.010580 0.972863 0.010084 28.329492
17 4 2 2021-06-09 23:55:38 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 49:84 2:3 59.717857 2.220913 2.572138 ... 0.399145 10.999128 0.354854 0.775108 0.045832 2.195005 1.555832 0.972639 0.015228 29.056988
18 4 3 2021-06-09 23:55:53 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 43:77 2:3 61.969221 2.026699 6.989458 ... 0.326731 10.956739 0.419218 0.753243 0.040568 2.095929 1.251544 0.976777 0.009427 28.313078
4 5 1 2021-06-09 23:24:18 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 19:57 2:3 53.010013 11.097434 -1.790824 ... 1.087683 10.965275 0.675722 0.822167 0.059414 4.036279 2.295310 0.952220 0.027352 33.355815
14 5 2 2021-06-09 23:41:45 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 44:82 2:3 64.717972 4.153035 -3.034680 ... 0.567947 11.448594 0.408139 0.769825 0.056204 4.103625 1.847953 0.966696 0.012619 32.529064
2 6 1 2021-06-09 23:24:11 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 45:81 2:3 62.953114 1.769023 -0.646246 ... 0.216321 11.513113 0.470660 0.792890 0.029588 1.260913 1.049494 0.965233 0.014776 30.644730
7 6 2 2021-06-09 23:24:21 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 89:125 2:3 64.823566 18.835219 13.113466 ... 1.159209 9.503113 2.506067 0.576338 0.152557 22.042768 32.322329 0.968538 0.032237 10.122137
5 6 3 2021-06-09 23:24:19 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 38:75 2:3 62.990802 2.049191 -2.338349 ... 0.298265 11.506661 0.596266 0.792194 0.041279 1.614134 1.158783 0.973527 0.010495 31.364216
3 6 4 2021-06-09 23:24:12 git-jca/3413-run-batch-session-c41958db922273a... /Users/julien/temp/neuromod/data_processed/sub... 58:95 2:3 63.925810 2.765595 -1.132526 ... 0.248317 11.727604 0.490648 0.803257 0.028672 1.754369 1.049329 0.971605 0.012450 31.247426

19 rows × 24 columns

fig_spine = Plot(dataset, plot_name = 'new-fig-2')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'

fig_spine.display('jupyter-book', tissue = 'WM')

   Subject Session            Timestamp  \
1        1       1  2021-06-09 23:20:54   
4        1       2  2021-06-09 23:21:02   
0        1       3  2021-06-09 23:20:52   
8        2       1  2021-06-09 23:38:23   
10       2       2  2021-06-09 23:38:28   
15       2       3  2021-06-09 23:48:42   
12       2       4  2021-06-09 23:38:42   
9        3       1  2021-06-09 23:38:25   
13       3       2  2021-06-09 23:38:46   
11       3       3  2021-06-09 23:38:40   
16       3       4  2021-06-09 23:53:25   
17       4       2  2021-06-09 23:53:48   
18       4       3  2021-06-09 23:54:02   
5        5       1  2021-06-09 23:21:05   
14       5       2  2021-06-09 23:38:47   
2        6       1  2021-06-09 23:20:55   
7        6       2  2021-06-09 23:21:12   
6        6       3  2021-06-09 23:21:05   
3        6       4  2021-06-09 23:21:00   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...      160:201       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...      162:203       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...      161:203       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...      157:193       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...      156:191       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...      159:193       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...      160:193       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...      141:177       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...      162:198       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...      161:196       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...      164:199       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...      159:196       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...      154:191       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...      166:201       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...      167:203       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    80.312877   1.602798       -3.958454  ...          0.148831   
4    80.768423   1.967870       -5.074403  ...          0.180384   
0    80.774162   3.246713       -3.760068  ...          0.174290   
8    92.724125   7.198446       -0.533592  ...          0.500942   
10   94.587712   7.628431       -0.855157  ...          0.571808   
15   92.666900   8.162162       -0.596256  ...          0.609800   
12   93.571468   6.715923       -1.310382  ...          0.499746   
9    73.617773   1.283275       -0.176559  ...          0.162039   
13   72.980170   1.733563       -0.169089  ...          0.218192   
11   70.593648   1.455799       -0.991364  ...          0.267249   
16   71.268228   1.688296        0.149827  ...          0.272076   
17   74.732375   0.995570       -0.057076  ...          0.173023   
18   75.005645   0.909686        4.142686  ...          0.251494   
5    70.779953   4.773098       -1.899860  ...          0.773255   
14   74.857807   2.759146       -2.745917  ...          0.388765   
2    72.958267   2.394267       -0.230000  ...          0.206093   
7    73.129881   1.990473       -0.959923  ...          0.223915   
6    73.894805   2.227882        0.547178  ...          0.174199   
3    72.129244   2.513562       -2.145414  ...          0.180008   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           11.899994          0.348936            0.689786   
4           11.935064          0.352203            0.692630   
0           11.942165          0.386189            0.692055   
8           13.469831          0.903365            0.749762   
10          13.618790          0.856929            0.751709   
15          13.567128          0.933170            0.758917   
12          13.510144          0.754180            0.750687   
9           11.618506          0.249626            0.719638   
13          11.669006          0.227977            0.728585   
11          11.246244          0.328627            0.702012   
16          11.275181          0.260300            0.698106   
17          12.063074          0.345358            0.754853   
18          11.967497          0.381923            0.743363   
5           12.190368          0.565430            0.779750   
14          12.401970          0.406430            0.775455   
2           12.298752          0.455764            0.786437   
7           12.384761          0.445033            0.792261   
6           12.449794          0.470167            0.792112   
3           12.327045          0.417297            0.794967   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.032309           3.342223          1.895299        0.973535   
4            0.031759           2.725679          1.980338        0.974296   
0            0.028034           4.826952          2.124976        0.973148   
8            0.061652           3.007144          1.340842        0.970252   
10           0.060540           2.065212          1.229055        0.970512   
15           0.066758           1.366771          1.115320        0.969417   
12           0.055164           1.432686          1.105488        0.970806   
9            0.026723           1.350991          0.866047        0.970433   
13           0.027002           1.021736          0.860224        0.971586   
11           0.046127           1.260142          1.145153        0.970805   
16           0.041606           1.752418          1.216747        0.975077   
17           0.027804           2.550164          1.247343        0.967420   
18           0.040588           1.571435          1.604254        0.972454   
5            0.071128           3.074997          1.954591        0.956469   
14           0.041603           2.156050          1.223840        0.966862   
2            0.025628           0.972269          0.813403        0.972373   
7            0.026887           1.640786          1.149530        0.970194   
6            0.023507           1.604021          1.084022        0.967781   
3            0.019853           1.783156          0.920410        0.969491   

    STD(solidity)  SUM(length)  
1        0.009511    33.716889  
4        0.007769    33.951292  
0        0.006615    34.526392  
8        0.010245    31.142010  
10       0.010239    30.640014  
15       0.010025    29.350071  
12       0.009661    28.757132  
9        0.008960    29.966024  
13       0.007557    29.619905  
11       0.008657    29.249095  
16       0.009043    30.022830  
17       0.011174    29.705806  
18       0.008886    28.928858  
5        0.019386    31.359579  
14       0.013124    31.380837  
2        0.010028    30.494727  
7        0.011049    30.874411  
6        0.010371    29.962644  
3        0.009872    30.558270  

[19 rows x 24 columns]
[[80.31287669419582, 80.7684228622334, 80.77416179502649, -100], [92.72412473358578, 94.58771243953994, 92.66689980123054, 93.57146821082088], [73.61777268131331, 72.98017043131877, 70.59364812603286, 71.2682278628924], [-100, 74.7323749938961, 75.00564528070014, -100], [70.77995321551784, 74.85780653908817, -100, -100], [72.95826654799964, 73.12988138337275, 73.89480466120321, 72.12924398136843]]

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